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NCBI C++ ToolKit: src/gui/widgets/aln_multiple/align_row.cpp Source File

<void()>

;

m_ConsensusRow(

),

m_bExpanded(

),

m_fExtOrgLookup(

),

m_PixLeft(-1), m_PixRight(-1), m_ModelLeft(-1), m_ModelRight(-1)

(aln_from > aln_to)

(aln_from, aln_to);

aln_from = floor(aln_from);

aln_to = floor(aln_to );

rc_right = floor(source_rc_vis.

());

rc_left = floor(source_rc_vis.

());

(aln_to == rc_right) {

(aln_from == rc_left) {

(aln_from == rc_left) {

(aln_to == rc_right) {

s_row,

,

);

}

(std::exception& e) {

(!

.empty()) {

wxEventType

=

.GetEventType();

wxPoint pos =

.GetPosition();

.Skip(

);

wxPoint pos =

.GetPosition();

(

== wxEVT_LEFT_DOWN) {

}

(

== wxEVT_LEFT_UP) {

skipped = glyph->

(hit_point);

(!event.CmdDown()) {

sel_visitor->

();

}

(

== wxEVT_LEFT_DCLICK) {

.Skip(skipped);

tooltip.

(

);

tooltip.

(

);

tooltip.

(

);

tooltip.

(

);

tooltip.

(

);

tooltip.

(

);

tooltip.

(sequence::CDeflineGenerator().GenerateDefline(handle));

(handle.

()) {

s_tip =

;

s_tip =

;

s_tip =

;

<

(

& pane)>&

)

TRangeData = tuple < IAlnExplorer::TSignedRange, IAlnExplorer::TSignedRange, COpenRange<double> >;

vector <TRangeData> render_list;

(; *align_it; ++(*align_it)) {

& seq_range = seg.

();

(seq_range.Empty())

(aln_range.Empty())

x1 = aln_range.

();

x2 = aln_range.GetTo();

x1 = (x1 - offset_x) / scale_x;

x2 = (x2 - offset_x + 1) / scale_x;

x1 = max<TModelUnit>(x1 + left, left);

x2 = min<TModelUnit>(x2 + left, right);

(

&

: render_list) {

& seq_range = get<0>(

);

& aln_range = get<1>(

);

& view_range = get<2>(

);

viewport.

(view_range.GetFrom(), view_range.GetTo());

= view_range.GetFrom(),

= view_range.GetTo();

(m_PixRight <= l || m_PixLeft >=

)

= (

-

) + 1;

seq_range.GetFrom(), seq_range.GetTo(),

=

(target_pane);

hit_point = track_pane.

(vp_pt.

(), vp_pt.

());

layout_track_hit;

(hit_point.

< 0)

glyph =

->CGlyphContainer::HitTest(hit_point);

glyph->

(hit_point, *track_tooltip, s_tip);

(!track_tooltip->IsEmpty()) {

tooltip.

(*track_tooltip);

s_tip +=

;

tooltip.

(*track_tooltip);

formatter->Render();

kMaxRegions = 5;

(n_regions < kMaxRegions) {

(n_regions < kMaxRegions) {

(seq_from > seq_to)

(seq_from, seq_to);

(aln_from > aln_to)

(aln_from, aln_to);

}

(aligned) {

(aln_r.

() == prev_aln_to + 1 && seq_r.

() > prev_to + 1) {

(n_regions < kMaxRegions) {

prev_aln_to = aln_r.

();

prev_to = seq_r.

();

(n_regions > kMaxRegions)

(

seqdesc : descr.

()) {

(seqdesc->IsTitle()) {

res = seqdesc->GetTitle();

(

seqdesc : descr.

()) {

(seqdesc->IsSource()) {

(subsrc->IsSetSubtype() && subsrc->GetSubtype() == subtype) {

subsrc->GetName();

(

seqdesc : descr.

()) {

(seqdesc->IsSource()) {

(

orgmod : on.

()) {

(orgmod->IsSetSubtype() &&

orgmod->GetSubname();

(!title.empty()) {

s_tip +=

;

s_tip +=

;

s_tip +=

;

tooltip.

(

, taxonomy);

s_tip +=

;

(!s.empty()) tooltip.

(

, s);

(!s.empty()) tooltip.

(

, s);

(!s.empty()) tooltip.

(

, s);

(!s.empty()) tooltip.

(

, s);

(!s.empty()) tooltip.

(

, s);

seq_pos /= base_width;

s_tip +=

;

tooltip.

(

, s_tip);

s_tip +=

;

tooltip.

(

, s_tip);

s_tip =

;

s_tip +=

;

seq +=

+ right_seq;

left = (

) floor(rc_model.

());

right =

(ceil(rc_model.

())) - 1;

can_render_scores = averageable || scale_x <

;

(has_scores && can_render_scores) {

start = (left < floor(rc_model.

())) ? left + 1 : left;

stop = (

)ceil(rc_model.

());

(stop + 1 > rc_model.

()) {

gl.

(orig_vp[0], orig_vp[1], orig_vp[2], orig_vp[3]);

gl.

(GL_LINES);

gl.

((

)rc_vp.Right(), (

)rc_vp.Top() + 1);

gl.

((

)rc_vp.Right(), (

)rc_vp.Bottom() - 1);

cl_insert(0.0f, 0.0f, 1.0f);

cl_unaligned(0.0f, 0.5f, 0.0f);

gl.

(GL_LINES);

ins_pos = it_2->GetAlnRange().GetFrom() - offset_x;

(ins_pos < row_start || ins_pos > row_stop)

gl.

(cl_unaligned);

log_len =

(log_len, kMinLen);

(ins_pos, top_y - 1, ins_pos, bottom_y - 1);

(x1, top_y - 1, x2, top_y - 1);

(x1, bottom_y, x2, bottom_y);

vector<TSeqRange> gaps;

empty_seg = (

.GetFrom() < row_start ||

.GetTo() > row_stop);

gaps.emplace_back(

.GetFrom(),

.GetTo());

(

.GetFrom() - gaps.back().GetTo() == 1) {

gaps.back().

(

.GetTo());

gaps.emplace_back(

.GetFrom(),

.GetTo());

(!gaps.empty()) {

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_LINES);

(

&

: gaps) {

pix_len =

.GetLength();

(pix_len < 1.5) {

pos =

.GetFrom() - offset_x;

alpha = 0.25 +

.GetLength() * 0.75;

gl.

(cl_unaligned);

gl.

(GL_LINES);

(aln_r.

() == prev_aln_pos + 1 &&

.GetFrom() > prev_pos + 1) {

log_len =

(log_len, kMinLen);

(ins_pos, top_y, ins_pos, bottom_y);

(x1, top_y, x2, top_y);

(x1, bottom_y, x2, bottom_y);

prev_aln_pos = aln_r.

();

prev_pos =

.GetTo();

(

& dst,

& src,

fraction,

long_seg)

dst += src * fraction;

TR rasterizer(rc_vp.Left(), rc_vp.Right(), rc_vis.

(), rc_vis.

());

( ; it; ++it ) {

rasterizer.AddInterval(

.GetFrom(),

.GetToOpen(), 1.0, f_sum);

vp_top_y = rc_vp.Top();

TR::TRaster& raster = rasterizer.GetRaster();

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

off_x = rc_vp.Left();

eps = 0.001f;

(!row_range.

()) {

y_c = floor((

(vp_top_y + vp_bottom_y) / 2) + 0.5);

gl.

(GL_LINES);

(row_start + off_x, y_c, row_stop + off_x, y_c);

(

= 0;

< raster.size(); ) {

v = raster[

];

(

< raster.size() && raster[

] == v) {

alpha = 0.25 + v * 0.75;

gl.

(start + off_x, vp_top_y,

+ off_x, vp_bottom_y);

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

vp_top_y = rc_vp.Top();

range_from = (

) (floor(rc_vis.

()));

CScoreCache::TScoreColl::const_iterator it = ScoreColl.

();

CScoreCache::TScoreColl::const_iterator it_end = ScoreColl.

();

it = ScoreColl.

(it, it_end, range_from);

eps = 0.00001f;

CScoreCache::TScoreColl::const_iterator it,

CScoreCache::TScoreColl::const_iterator it_end,

vp_top_y,

vp_bottom_y)

eps = 0.001f;

(it_seg && it != it_end && it->GetFrom() <= rc_vis.

()) {

from = std::max<int>(

.GetFrom(), it->GetFrom());

to = std::min<int>(

.GetTo(), it->GetTo());

pix = { 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,

};

empty_seg = (from < row_start || to > row_stop);

rasterizer.AddInterval(from, to + 1, pix, f_sum);

}

(!empty_seg && ((to - from) + 1) > 0) {

rasterizer.AddInterval(from, to + 1, pix, f_sum);

(to ==

.GetTo())

(to == (

) it->GetTo())

TR::TRaster& raster = rasterizer.GetRaster();

shift_x = rc_vp.

();

value_scale = value_limits.

() - value_limits.

();

(value_scale <= 0)

y_c = floor((

(vp_top_y + vp_bottom_y ) / 2) + 0.5);

(

= 0;

< raster.size(); ) {

x1 =

+ shift_x;

& sc_pix = raster[

];

(

< raster.size() && raster[

] == sc_pix) {

x2 =

+ shift_x;

kAmbiguousResidueColor(

);

= kAmbiguousResidueColor;

sc =

(1.0, max<double>(0., ((sc - value_limits.

()) / value_scale)));

alpha = 1.0f - sc * 0.75f;

gl.

(x1, vp_top_y, x2, vp_bottom_y);

}

(sc_pix.

> eps) {

gl.

(x1, y_c - 1, x2, y_c + 1);

CScoreCache::TScoreColl::const_iterator it,

CScoreCache::TScoreColl::const_iterator it_end,

vp_top_y,

vp_bottom_y)

pix = { 0.0f, 0.0f,

};

(it_seg && it != it_end && it->GetFrom() <= rc_vis.

()) {

from = std::max<int>(

.GetFrom(), it->GetFrom());

to = std::min<int>(

.GetTo(), it->GetTo());

empty_seg = (from < row_start || to > row_stop);

(to ==

.GetTo()) {

(to == (

) it->GetTo()) {

TR::TRaster& raster = rasterizer.GetRaster();

y_c = floor((

(vp_top_y + vp_bottom_y ) / 2) + 0.5);

eps = 0.0001f;

shift_x = rc_vp.

();

(

= 0;

< raster.size(); ) {

& sc_pix = raster[

];

(++

< raster.size() && raster[

] == sc_pix) ;

(sc_pix.

) {

gl.

(start + shift_x, y_c - 1 ,

+ shift_x, y_c + 1);

gl.

(start + shift_x, vp_top_y,

+ shift_x, vp_bottom_y + 1);

min_w >= scale_x;

}

;

(

ch) {

ch ==

; }

start,

stop)

unique_ptr<IAlnSegmentIterator> p_it(

off_y = floor(off_y/2. + 0.5);

render_scores =

;

render_scores = method &&

stop = aln_r.GetTo();

sStart = seq_r.

();

sStop = seq_r.GetTo();

(base_width == 3) {

frame_shift_f = sStart % base_width;

frame_shift_t = 2 - sStop % base_width;

(base_width == 3) {

vector<CRgbaColor*>

;

(render_scores) {

CScoreCache::TScoreColl::const_iterator it = ScoreColl.

();

CScoreCache::TScoreColl::const_iterator it_end = ScoreColl.

();

it = ScoreColl.

(it, it_end, start);

= stop - start + 1;

std::fill_n(

.begin(),

, &default_color);

(; it != it_end; ++it) {

std::fill_n(

.begin() + (from - start), to - from + 1, &cl);

has_consensus =

;

(consensus.length() == seq.length())) {

has_consensus =

;

has_colors = (

.size() == seq.length());

text_char(

);

center_y = (top_y + bottom_y) * 0.5 + 0.5;

base_h = double(base_width)/2.;

(

= 0;

< seq.size(); ++

) {

current_color = has_colors ? *

[

] : default_color;

(has_consensus && seq[

] !=

&& consensus[

] == seq[

]) {

render_dot = dot_texture.

();

gl.

(GL_TEXTURE_2D);

w = dot_texture->GetImage()->GetWidth();

dot_texture->MakeCurrent();

current_color.

(0.65f);

gl.

(current_color);

gl.

(GL_LINES);

gl.

(current_color);

text_char[0] = seq[

];

gl.

(x - off_x, y, text_char.c_str());

base_height = 0;

height =

(rc_vp.

()) - 1;

offset_top = (rc_vp.

() - row_top);

top = rc_vp.

();

(offset_top >= 0) {

top -= (offset_top + base_height);

model_top =

(offset_top);

model_bottom = model_top + rc_vp.

();

rc_vis.

(model_bottom, model_top);

model_height > 0;

(!

().IsPrinterFriendly()) {

y_top = rc_vp.Top() - h;

(

= 0;

< 3;

++ ) {

(vp_pt.

() >= left && vp_pt.

() < left +

) {

gl.

(rc_vp.Left(), rc_vp.Bottom(), rc_vp.Right(), rc_vp.Top());

half = rc_btn.

() / 2;

x1 = rc_btn.

();

x2 = rc_btn.

();

gl.

(GL_TRIANGLES);

gl.

(GL_LINES);

half = rc_btn.

() / 2;

x1 = rc_btn.

();

x2 = rc_btn.

();

gl.

(GL_TRIANGLES);

gl.

(GL_LINES);

*s_marker =

;

(seq_pos == -1) {

.append(s_marker);

gl.

(rc_vp.Left(), rc_vp.Bottom(), rc_vp.Right(), rc_vp.Top());

gl.

(GL_LINES);

gl.

(rc_vp.Right(), rc_vp.Top());

gl.

(rc_vp.Right(), rc_vp.Bottom());

gl.

(rc_vp.Left(), rc_vp.Bottom());

gl.

(rc_vp.Right(), rc_vp.Bottom());

->SetOverviewCutoff(gConfig->GetOverviewCutoff());

}

(exception& e) {

aln_pos = (

) floor(rc_vis.

());

aln_pos = -1 + (

) ceil(rc_vis.

());

pos = (pos / 3) * 3;

( alstart < alstop ){

alrange.

( alstart, alstop);

alrange.

( alstop, alstart);

(!aln_r.Empty()) {

aligned += seq_r.GetLength();

(aln_r.GetFrom() == prev_aln_to + 1 && seq_r.GetFrom() > prev_seq_to + 1) {

unaligned += seq_r.GetFrom() - prev_seq_to;

indel += seq_r.GetLength();

prev_aln_to = aln_r.GetTo();

prev_seq_to = seq_r.GetTo();

gap += aln_r.GetLength();

indel += aln_r.GetLength();

unaligned += aln_r.GetLength();

start /= base_width;

aln_str =

;

aln_str += (is_aa) ?

:

;

tooltip.

(aln_str);

bases = is_aa ?

:

;

track.

(last_hit_track.GetPointer());

vr.SetHorz(

,

);

(max_height > 0) {

widget->PopupMenu(menu);

widget->PushEventHandler(

);

widget->PopEventHandler();

gConfig->SetDirty(

);

bottom = top - (

- 1);

static IGlFont::EAlignMode s_GetColumnAlignemnt(int col_type)

double CompressLength(double len)

static string s_GetSourceSubtype(const CSeq_descr &descr, CSubSource::ESubtype subtype)

static string s_GetTitle(const CSeq_descr &descr)

static const int kTextOffsetY

static const int kAlignSpace

height of "white-space" between row borders and alignment band

static const int kSeqVertSpace

static const int kTextVertSpace

USING_SCOPE(ncbi::objects)

static const int kTooltipMaxLines

ON_EVENT(CGraphNotification, CGraphNotification::eContentChanged, &CAlnVecRow::x_OnGraphContentChanged) ON_EVENT(CGraphNotification

static const int kMaxSeqInTooltip

static const int kTextOffsetX

static const int kButtonSignSize

string FormatRange(TSignedSeqPos from, TSignedSeqPos to)

#define TOOLTIP_RANGE_PIX

static const int kGapOffset

vertical offset from the border of the alignment band to the border of gap band

static const TModelUnit kScoreMinScale

static void s_PrepareTrackPane(TModelUnit aln_from, TModelUnit aln_to, TModelUnit seq_from, TModelUnit seq_to, const IAlignRowHandle &row_handle, const CGlPane &source_pane, CGlPane &target_pane)

static const int kButtonSize

static const int kButtonOffset

static void FSetPixMaxCoverage(SScPix &dst, const SScPix &src, float fraction, bool long_seg)

a pixel with the Max coverage (fraction) overrides all attributes

void glLined(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2)

static string s_GetOrgModNatHost(const CSeq_descr &descr)

static const int kPosOffsetX

ncbi::TMaskedQueryRegions mask

virtual int GetRowState() const

Returns row state (combination of EState flags)

CAlnRowState()

CAlnRowState.

virtual void SetRowState(int mask, bool b_set)

Set/Clear Row State.

class CAlnVecRow - implementation of IAlignRow for CAlnVec-based alignments.

const CRowDisplayStyle * m_Style

const IAlignRowHandle & m_Handle

void x_ForEachAlnSeg(const IAlnExplorer::TSignedRange &range, const CGlPane &src_pane, CGlPane &target_pane, const function< bool(CGlPane &pane)> &f)

virtual int GetRowNum() const

Returns index of row in IAlnMultiDataSource.

void ConfigureTracks(bool reset=false)

virtual void x_RenderIconStrand()

virtual void x_RenderAlign()

Renders graphical part of the row.

TVPUnit m_PixLeft

Graphics caching.

void x_RenderTracks(CGlPane &pane, const TSignedRange &range)

virtual void UpdateOnStyleChanged()

virtual TSeqPos GetColumnAsSeqPos(TColumnType type, const TModelRect &rc_vis) const

virtual void x_RenderNonAveragableScores(CGlPane &pane, IAlnSegmentIterator &it_seg, TScoreConstIterator it, const TScoreConstIterator it_end, int vp_top_y, int vp_bottom_y)

virtual void GetHTMLActiveAreas(TColumnType col_type, CGlPane &pane, TAreaVector &areas)

virtual void x_OnClickExpandBtn(CGlPane &pane)

virtual TVPRect x_GetButtonRect(EButtons btn, int shift=1)

virtual void OnMouseEvent(wxMouseEvent &event, TColumnType col_type, CGlPane &pane)

void x_GetAlnPosLabel(TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir, string &label) const

virtual void x_RenderAveragableScores(CGlPane &pane, IAlnSegmentIterator &it_seg, TScoreConstIterator it, const TScoreConstIterator it_end, int vp_top_y, int vp_bottom_y)

virtual void x_RenderGraph(const TSignedRange &range)

string x_GetTooltipSequence(TSeqPos from, TSeqPos to)

void GetTaxonomy(string &taxonomy) const

virtual void x_GetIconsTooltip(const TVPPoint &pt, CGlPane &pane, ITooltipFormatter &tooltip)

void x_GetAlignmentTooltip_Gap(const TSignedSeqRange &aln_r, const TSignedSeqRange &seq_r, ITooltipFormatter &tooltip)

virtual float GetColumnAsFloat(TColumnType type) const

virtual void x_UpdateRowHeight()

virtual bool x_CanRenderSeq(CGlPane &pane)

Checks if sequence can be drawn.

virtual void x_RenderIconExpand()

void x_GetAlignmentTooltip_Insert(const TSignedSeqRange &aln_r, const TSignedSeqRange &seq_r, ITooltipFormatter &tooltip)

virtual void UseExternalOrganismLookup(bool f)

virtual void x_RenderDescr()

virtual void LTH_ConfigureTracksDlg(const string &category)

CRef< CFeaturePanel > m_TrackPanel

void ConfigureTracksDialog(const string &category=NcbiEmptyString)

virtual void x_CreateTrackPanel(CGlPane &pane)

virtual void GetTooltip(const TVPPoint &vp_pt, TColumnType col_type, CGlPane &pane, ITooltipFormatter &tooltip)

returns tooltip text by point in the viewport coordinates

AutoPtr< CLayoutTrackHandler > m_TrackHandler

virtual void UpdateOnAnchorChanged()

virtual bool IsExpanded() const

CRef< CSeqGlyph > x_HitTest(const TVPPoint &vp_pt, CGlPane &pane, TModelPoint &hit_point)

bool m_NeedUpdateSelection

unique_ptr< CGlPane > m_TrackPane

virtual void LTH_PushEventHandler(wxEvtHandler *handler)

virtual string & GetColumnText(TColumnType col_type, string &text, bool for_printer=false) const

unique_ptr< CRenderingContext > m_RenderingCtx

virtual void GHH_Redraw()

redraws the Host and the handler

void x_GetAlignmentTooltip_Unaligned(TSignedSeqPos aln_prev_to, TSignedSeqPos aln_from, TSignedSeqPos prev_to, TSignedSeqPos from, ITooltipFormatter &tooltip)

virtual EButtons x_HitTestButton(CGlPane &pane, const TVPPoint &pt)

virtual void GHH_ReleaseMouse()

releases captured mouse

virtual int x_GetBaseHeight() const

virtual void GHH_CaptureMouse()

captures mouse events in the hosting window for D&D

virtual void x_RenderSequence(CGlPane &pane, TModelUnit top_y, TModelUnit bottom_y, int start, int stop)

virtual void GHH_SetCursor(const wxCursor &cursor)

changes the cursor in the hosting window

virtual void PrepareRendering(CGlPane &pane, TVPUnit row_top, int state)

virtual void Update(const CGlPane &pane, bool layout_only=false)

virtual void SetDisplayStyle(const CRowDisplayStyle *style)

virtual void LTH_OnLayoutChanged()

provides mouse coords in OpenGL viewport coord system

virtual bool IsExpandable() const

virtual void LTH_PopEventHandler()

virtual bool IsNucProtAlignment() const

virtual void SetHost(IAlignRowHost *host)

void x_OnGraphSizeChanged(CEvent *evt)

virtual void SetScoreCache(CScoreCache *cache)

virtual const IAlnRowGraphProperties * GetProperties() const

virtual void x_GetDescrTooltip(const TVPPoint &pt, CGlPane &pane, ITooltipFormatter &tooltip)

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const

CWeakRef< CLayoutTrack > m_LastHitTrack

virtual void x_RenderAlignSegments(CGlPane &pane, IAlnSegmentIterator &it_seg, TModelUnit top_y, TModelUnit bottom_y, const CRgbaColor &color)

virtual void x_RenderIcons()

virtual void x_GetAlignmentTooltip(const TVPPoint &pt, CGlPane &pane, ITooltipFormatter &tooltip)

virtual void x_RenderAlnPos(TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir)

virtual TModelPoint THH_GetModelByWindow(const wxPoint &pt)

virtual string GetAlignmentTooltip(TSeqPos pos, TSeqPos half_width)

IAlignRowHost * x_GetHost()

virtual void x_ResetTrackPanel()

virtual void x_RenderAlignScores(IAlnSegmentIterator &it_seg, int top_y, int bottom_y, bool averageable)

void x_OnGraphContentChanged(CEvent *evt)

virtual void x_RenderInserts(CGlPane &pane, int from, int to, TModelUnit top_y, TModelUnit bottom_y)

virtual bool UsesAATranslation() const

virtual void x_RenderTextCell(const string &text, IGlFont::TAlign align)

bool x_InitTrackPane(const CGlPane &row_pane, CGlPane &track_pane)

IAlnExplorer::TSignedRange TSignedRange

virtual void SetProperties(IAlnRowGraphProperties *props)

virtual void RenderColumn(TColumnType col_type)

Renders a row cell corresponding to column specified by "col_type".

void x_GetAlignmentTooltip_Helper(TSeqPos pos, TSignedRange &range, ITooltipFormatter &tooltip)

virtual void x_RenderEmptyBox()

size_t GetTrackCount(CGlPane &pane)

CAlnVecRow(const IAlignRowHandle &handle)

CAlnVecRow.

virtual void LTH_PopupMenu(wxMenu *menu)

show track-specific context menu.

void x_GetAlignmentTooltip_General(TSeqPos pos, ITooltipFormatter &tooltip)

virtual string & GetStringAtPos(string &buffer, TSignedSeqPos aln_pos) const

virtual void x_RenderUnaligned(CGlPane &pane, int from, int to, TModelUnit top_y, TModelUnit bottom_y)

CConsensusRow * m_ConsensusRow

CScoreCache * m_Cache

row display style

unique_ptr< CRenderingContext > m_SequenceRenderingCtx

virtual const CRowDisplayStyle * GetDisplayStyle()

virtual void GetRowStatistics(ITooltipFormatter &tooltip) const

virtual void Expand(bool b_exp, CGlPane &pane)

virtual CRef< CLayoutTrack > THH_GetLayoutTrack()

Get the layout track under the current mouse position.

virtual int GetHeightPixels() const

Returns height of the row in pixels.

const COrgName & GetOrgname(void) const

bool IsSetOrgname(void) const

const IAlignRowHandle & GetHandle() const

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const

CEvent - generic event implementation TODO TODO - Attachments.

void SetInputObject(SConstScopedObject &obj)

void SetConfigKey(const string &config_key)

virtual void Update(bool layout_only)

Update content and layout including the bounding box.

virtual CRef< CSeqGlyph > HitTest(const TModelPoint &p)

Hit testing.

void LoadDefaultTracks()

Reset tracks to the original default track list.

void ShowConfigureTracksDlg(const string &category)

void SetTrackConfig(const TTrackSettingsSet &settings_set)

void SetDSContext(ISGDataSourceContext *ds_ctx)

CGlAttrGuard - guard class for restoring OpenGL attributes.

const CLayoutGroup & GetGroup() const

void SaveSettings(const string &curr_color, const string &curr_size) const

size_t GetChildrenNum() const

Get total number of children.

CLayoutTrackHandler - is the handler for handling the user interactions on layout tracks.

void Render(CGlPane &pane)

void SetHost(ITrackHandlerHost *host)

CLayoutTrackHandler inline methods.

virtual void SetPane(CGlPane *pane)

void SetConfig(CRef< CSeqGraphicConfig > conf)

void SetProfile(const string &preset_style)

CLayoutTrack inline method implmentation.

void SetHost(ILayoutTrackHost *host)

void GetLabel(string *label) const

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

@ fSkipGrid

track frame will be rendered when triggered.

@ fSkipTitleBar

can be collpased and expanded.

@ fSkipControls

track frame will be rendered when triggered.

class CRgbaColor provides a simple abstraction for managing colors.

CRowDisplayStyle is a base class representing a display style for IAlignRow.

CRef< CSeqGraphicConfig > GetSeqGraphicConfig() const

CRef< CGlTexture > GetDotTexture() const

virtual const CRgbaColor & GetColor(TColorType type) const

int GetShownElements() const

const string & GetTrackConfigKey() const

virtual bool GetShowIdenticalBases(void) const

const CTrackConfigManager::TTrackProxies & GetTrackSettings() const

bool IsWebRendering() const

virtual const CGlTextureFont & GetTextFont(void) const

virtual const CGlTextureFont & GetSeqFont(void) const

static const string & DefTrackProfile()

static bool IsBackgroundJob()

bool HasScores() const

returns "true" if CalculateScores() did produce results

const TScoreColl & GetScores(TNumrow row) const

IScoringMethod::TScore TScore

IScoringMethod * GetScoringMethod()

const CRgbaColor & GetColorForScore(TScore score, IScoringMethod::EColorType type) const

class CSelectionVisitor is a concrete glyph visitor for selection traversal and deselection traversal...

void UpdateSelection(CSeqGlyph *glyph)

void ResetObjectSelection(CSeqGlyph *glyph)

void SelectObject(const CObject *obj, bool verified)

bool IsObjectSelected(const CObject *obj)

void DeSelectObject(const CObject *obj)

bool HasSelectedObjects() const

virtual void SetHeight(TModelUnit h)

virtual bool IsClickable() const

Query if this glyph is clickable.

virtual void GetTooltip(const TModelPoint &, ITooltipFormatter &tt, string &t_title) const

Get the tooltip if available.

virtual bool OnLeftUp(const TModelPoint &)

virtual bool OnLeftDblClick(const TModelPoint &)

virtual TModelUnit GetHeight() const

virtual bool OnLeftDown(const TModelPoint &)

void Draw() const

render the layout.

CRef< CHistParamsManager > GetHistParamsManager() const

Get histogram config manager.

void SetTrackProfile(const string &profile)

@Seq_descr.hpp User-defined methods of the data storage class.

CTempTrackProxy::TTrackProxies TTrackProxies

bool IsTrackInitDone() const

FSetPix2(bool sequence_level)

void operator()(SScPix2 &dst, const SScPix2 &src, float fraction, bool long_seg)

accumulate weighted scores

IAlignRowHandle provides an abstract way to access alignment row data.

virtual bool UsesAATranslation() const =0

virtual int GetMismatches() const

virtual TSignedSeqPos GetSeqStart() const =0

virtual void GetHost(string &value) const

virtual bool CanGetBioseqHandle() const =0

virtual bool IsAnchor() const

virtual const string & GetOrgLabel(bool fExtOrgLookup=false) const

virtual TSignedSeqPos GetSeqAlnStart() const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle() const =0

virtual void GetCountry(string &value) const

virtual double GetPctCoverage() const

virtual bool IsNucProtAlignment() const =0

virtual double GetPctIdentity() const

virtual size_t GetBaseWidth() const =0

virtual IAlnExplorer::TSignedRange GetSeqAlnRange() const =0

virtual TSeqPos GetSeqLength() const

virtual TSignedSeqPos GetSeqPosFromAlnPos(TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual TNumrow GetRowNum() const =0

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const =0

virtual TSignedSeqPos GetSeqAlnStop() const =0

virtual TSignedSeqPos GetSeqStop() const =0

virtual void GetCollectionDate(string &value) const

virtual string & GetSeqString(string &buffer, const IAlnExplorer::TRange &seq_rng) const =0

virtual void GetIsolationSource(string &value) const

virtual bool IsNegativeStrand() const =0

virtual void GetTaxonomy(string &taxonomy, bool fExtOrgLookup=false) const

virtual TSignedSeqPos GetAlnPosFromSeqPos(TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

virtual void GetGeneSymbol(string &value) const

virtual const string & GetText() const =0

IAlignRowHost represents a context in which IAlignRow lives.

virtual void ARH_OnSelectionChanged()=0

notifies a host about selection change

virtual CSelectionVisitor * ARH_GetSelectionVisitor()=0

notifies a host about selection change

virtual int ARH_GetRowTop(IAlignRow *p_row)=0

Returns Y-pos for row.

virtual TVPPoint ARH_GetVPPosByWindowPos(const wxPoint &pos)=0

provides mouse coords in OpenGL viewport coord system

virtual void ARH_OnRowChanged(IAlignRow *row)=0

notifies a host about changes the row

@ fWidgetFocused

it isn'e exactly a row state;

vector< CHTMLActiveArea > TAreaVector

@ ePctIdentity

% identity to consensus or anchor

@ eIconStrand

Icon for Positive/Negative (Mixed?) strand.

@ eIconExpand

Icon for expand (+) button.

@ eIcons

Strand + Expand icons.

@ ePctCoverage

% coverage to anchor

@ eMismatches

% number of mismatches to anchor/consensus

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

Alignment segment iterator interface.

@ eSkipInserts

Iterate segments where at least some rows are aligned (including gap segments)

@ eInsertsOnly

Iterate only ranges not participating in the alignment (unaligned segments)

@ eAllSegments

Iterate all segments.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fAligned

Aligned segment.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

bool IsAligned(void) const

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

static const int kAmbiguousResidueScore

virtual void GHH_ReleaseMouse()=0

releases captured mouse

virtual void GHH_Redraw()=0

redraws the Host and the handler

virtual void GHH_CaptureMouse()=0

captures mouse events in the hosting window for D&D

virtual void GHH_SetCursor(const wxCursor &cursor)=0

changes the cursor in the hosting window

virtual CConstRef< CObject > GetObject(TSeqPos pos) const =0

access our core component - we wrap an object(s) of some sort.

IScoringMethod represents an abstract algorithm for calculating alignment scores and assigning colors...

virtual int GetSupportedColorTypes() const =0

returns a combination of EColorType flags

virtual bool IsAverageable() const =0

return "true" if scores could be averaged

static const Colors colors

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

Include a standard set of the NCBI C++ Toolkit most basic headers.

static const char * str(char *buf, int n)

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_ASSERT(expr, mess)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

CGlRect & IntersectWith(const CGlRect &r)

void SetModelLimitsRect(const TModelRect &R)

virtual void Viewport(GLint x, GLint y, GLsizei width, GLsizei height)=0

void SetViewport(const TVPRect &R)

virtual void Enable(GLenum glstate)=0

EAlignMode

alignment modes

virtual void Begin(GLenum mode)=0

Start rendering.

virtual void BlendFunc(GLenum sfactor, GLenum dfactor)=0

Options to be used when GL_BLEND is enabled.

virtual void BeginClippingRect(GLint x, GLint y, GLsizei width, GLsizei height)=0

TModelUnit UnProjectWidth(TVPUnit vp_w) const

TModelPoint UnProject(TVPUnit m_x, TVPUnit m_y) const

void Color3d(GLdouble r, GLdouble g, GLdouble b)

IRender & GetGl()

convenience function for getting current render manager

void Vertex2d(GLdouble x, GLdouble y)

TVPRect & GetViewport(void)

virtual void BeginText(const CGlTextureFont *font, const CRgbaColor &color)=0

Text is drawn is pixel coordinates.

virtual TModelUnit GetFontDescender() const

static string FormatSeparatedNumber(int number, bool b_postfix=false)

virtual void EndText()=0

Pops matrices and attributes after writing text.

const TVPRect * GetClipRect() const

returns clipping rect or NULL (if there is no clipping)

TModelUnit UnProjectX(TVPUnit m_x) const

CGlPoint< T > CenterPoint() const

TModelRect & GetModelLimitsRect(void)

virtual void EndClippingRect()=0

bool PtInRect(T x, T y) const

virtual bool IsPrinterFriendly() const =0

virtual void End()=0

Finish rendering (create buffer and send to renderer)

virtual void PolygonMode(GLenum face, GLenum mode)=0

Set the polygon rasterization mode.

void SetVert(T bottom, T top)

void SetVisibleRect(const TModelRect &R)

virtual TModelUnit GetMetric(EMetric metric, const char *text=NULL, int len=-1) const

virtual void WriteText(TModelUnit x, TModelUnit y, const char *text, TModelUnit rotate_degrees=0.0)=0

Write text at specified model coords.

virtual TModelUnit TextWidth(const char *text) const

Compute and return font metrics.

virtual TModelUnit TextHeight(void) const

TModelRect & GetVisibleRect(void)

void Vertex2f(GLfloat x, GLfloat y)

virtual void Disable(GLenum glstate)=0

glDisable()

virtual void LineWidth(GLfloat w)=0

Set line width for drawing: glLineWidth()

TModelUnit GetScaleX(void) const

TModelUnit GetOffsetX() const

void SetExactOrthoProjection(bool exact_projection)

void SetHorz(T left, T right)

CGlPoint< TModelUnit > TModelPoint

virtual void ColorC(const CRgbaColor &c)=0

Set current color (glColor{3,4}{f,d}{v,})

void Rectd(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2)

void EnableOffset(bool b_en=true)

Offset is used as a workaround for OpenGL precision problems emerging when size of visible range is s...

virtual void GetViewport(GLint *params)=0

virtual void AddRow(const string &sContents="", unsigned colspan=2)=0

add a row with a cell, spanning across all columns

const_iterator end() const

void Lighten(float scale)

static CIRef< ITooltipFormatter > CreateTooltipFormatter()

static CRgbaColor Interpolate(const CRgbaColor &color1, const CRgbaColor &color2, float alpha)

Interpolate two colors.

#define END_EVENT_MAP()

Ends definition of Command Map.

const_iterator find(position_type pos) const

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

virtual void Append(const ITooltipFormatter &tooltip)=0

appends another formatter to this one

const_iterator begin() const

string GetProteinName(const CBioseq_Handle &seq)

Return protein name from corresponding Prot-ref feature.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

const TDescr & GetDescr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

bool CanGetDescr(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

TRefType Lock(void) const

Lock the object and return reference to it.

void Reset(void)

Reset the containing pointer to null.

position_type GetLength(void) const

TThisType & IntersectWith(const TThisType &r)

TThisType IntersectionWith(const TThisType &r) const

position_type GetToOpen(void) const

TThisType & Set(position_type from, position_type to)

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool IsSetSubtype(void) const

Check if a value has been assigned to Subtype data member.

@ eSubtype_collection_date

DD-MMM-YYYY format.

@ eSubtype_isolation_source

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TMod & GetMod(void) const

Get the Mod member data.

bool CanGetMod(void) const

Check if it is safe to call GetMod method.

@ eSubtype_nat_host

natural host of this specimen

const Tdata & Get(void) const

Get the member data.

unsigned int

A callback function used to compare two keys in a database.

if(yy_accept[yy_current_state])

static void text(MDB_val *v)

Defines: CTimeFormat - storage class for time format.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

void operator()(float &dst, const float &src, float fraction, bool long_seg)

~SRenderingContextGuard()

SRenderingContextGuard(const function< void()> &f)

represents a pixel with two scores, one corresponds to a gap interval, another - to an aligned segmen...

bool operator==(const SScPix2 &other) const

represents a pixel with a score, if several intervals cover a pixel, the interval with the maximum co...

float m_MaxCoverage

score assigned to the pixel

bool m_Gap

fraction of the pixel corresponding to the m_Score

bool operator==(const SScPix &other) const

true if this is a gap interval

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